HEADER DNA 24-MAR-09 2KH6 TITLE SOLUTION STRUCTURE OF CIS-5R,6S-THYMINE GLYCOL OPPOSITE COMPLEMENTARY TITLE 2 ADENINE IN DUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS THYMINE GLYCOL, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.L.BROWN REVDAT 3 01-MAY-24 2KH6 1 REMARK REVDAT 2 26-FEB-20 2KH6 1 REMARK LINK REVDAT 1 02-MAR-10 2KH6 0 JRNL AUTH K.L.BROWN,M.ROGINSKAYA,Y.ZOU,A.ALTAMIRANO,A.K.BASU,M.P.STONE JRNL TITL BINDING OF THE HUMAN NUCLEOTIDE EXCISION REPAIR PROTEINS XPA JRNL TITL 2 AND XPC/HR23B TO THE 5R-THYMINE GLYCOL LESION AND STRUCTURE JRNL TITL 3 OF THE CIS-(5R,6S) THYMINE GLYCOL EPIMER IN THE 5'-GTGG-3' JRNL TITL 4 SEQUENCE: DESTABILIZATION OF TWO BASE PAIRS AT THE LESION JRNL TITL 5 SITE JRNL REF NUCLEIC ACIDS RES. V. 38 428 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 19892827 JRNL DOI 10.1093/NAR/GKP844 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : DELAGLIO, ZHENGRONG AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KH6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000101115. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 278 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE-1, 100 MM REMARK 210 SODIUM CHLORIDE-2, 10 UM SODIUM REMARK 210 AZIDE-3, 50 UM EDTA-4, 100% D2O; REMARK 210 20 MM SODIUM PHOSPHATE-5, 100 MM REMARK 210 SODIUM CHLORIDE-6, 10 UM SODIUM REMARK 210 AZIDE-7, 50 UM EDTA-8, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 31P-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, MARDIGRAS, REMARK 210 CORMA, CURVES, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DT A 8 C3' DT A 8 C2' -0.060 REMARK 500 1 DT A 10 C3' DT A 10 C2' -0.078 REMARK 500 1 DT A 10 O3' DT A 10 C3' -0.051 REMARK 500 1 DC B 24 O3' DC B 24 C3' -0.068 REMARK 500 2 DC B 14 N3 DC B 14 C4 -0.043 REMARK 500 3 DG A 3 C2 DG A 3 N2 -0.061 REMARK 500 3 DG A 5 C2 DG A 5 N2 -0.061 REMARK 500 4 DC B 20 C4 DC B 20 N4 -0.058 REMARK 500 4 DC B 22 C3' DC B 22 C2' -0.078 REMARK 500 4 DC B 22 C2 DC B 22 O2 -0.055 REMARK 500 4 DC B 22 N3 DC B 22 C4 -0.046 REMARK 500 4 DA B 23 C6 DA B 23 N1 -0.048 REMARK 500 5 DG A 11 C2 DG A 11 N2 -0.061 REMARK 500 5 DA B 13 C6 DA B 13 N1 -0.048 REMARK 500 6 DG A 3 C2 DG A 3 N2 -0.061 REMARK 500 6 DG A 11 O3' DG A 11 C3' -0.067 REMARK 500 6 DC B 22 C3' DC B 22 C2' -0.050 REMARK 500 7 DG A 3 C2 DG A 3 N2 -0.063 REMARK 500 8 DT A 12 C3' DT A 12 C2' -0.048 REMARK 500 8 DT A 12 O3' DT A 12 C3' -0.052 REMARK 500 8 DA B 13 C2' DA B 13 C1' -0.071 REMARK 500 8 DA B 13 O4' DA B 13 C4' -0.075 REMARK 500 9 DG A 1 C5' DG A 1 C4' 0.055 REMARK 500 9 DA B 13 O4' DA B 13 C4' -0.065 REMARK 500 9 DC B 14 N3 DC B 14 C4 -0.044 REMARK 500 10 DA B 13 C6 DA B 13 N1 -0.044 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT A 2 OP1 - P - OP2 ANGL. DEV. = -15.5 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 2 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 3 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DC A 4 OP1 - P - OP2 ANGL. DEV. = -11.3 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 5 OP1 - P - OP2 ANGL. DEV. = -11.8 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 7 OP1 - P - OP2 ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DT A 8 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DT A 8 C3' - C2' - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DT A 9 OP1 - P - OP2 ANGL. DEV. = -12.4 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 10 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 11 OP1 - P - OP2 ANGL. DEV. = -11.6 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 12 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 13 C1' - O4' - C4' ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DA B 13 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA B 13 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 13 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 14 OP1 - P - OP2 ANGL. DEV. = -11.4 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA B 15 OP1 - P - OP2 ANGL. DEV. = -11.8 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA B 16 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DA B 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 16 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 17 OP1 - P - OP2 ANGL. DEV. = -14.8 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DC B 18 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC B 18 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DA B 19 OP1 - P - OP2 ANGL. DEV. = -12.6 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 20 OP1 - P - OP2 ANGL. DEV. = -13.6 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 629 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DA B 15 0.06 SIDE CHAIN REMARK 500 3 DG A 7 0.06 SIDE CHAIN REMARK 500 3 DT A 8 0.07 SIDE CHAIN REMARK 500 3 DG A 11 0.07 SIDE CHAIN REMARK 500 3 DC B 20 0.07 SIDE CHAIN REMARK 500 4 DT A 8 0.06 SIDE CHAIN REMARK 500 5 DA B 19 0.08 SIDE CHAIN REMARK 500 5 DC B 20 0.06 SIDE CHAIN REMARK 500 6 DT A 8 0.09 SIDE CHAIN REMARK 500 6 DA B 19 0.09 SIDE CHAIN REMARK 500 6 DA B 23 0.05 SIDE CHAIN REMARK 500 7 DG A 7 0.05 SIDE CHAIN REMARK 500 7 DT A 8 0.10 SIDE CHAIN REMARK 500 7 DA B 19 0.07 SIDE CHAIN REMARK 500 7 DC B 20 0.07 SIDE CHAIN REMARK 500 8 DT A 8 0.10 SIDE CHAIN REMARK 500 8 DA B 19 0.07 SIDE CHAIN REMARK 500 8 DC B 20 0.07 SIDE CHAIN REMARK 500 9 DG A 7 0.07 SIDE CHAIN REMARK 500 9 DT A 8 0.08 SIDE CHAIN REMARK 500 9 DA B 19 0.06 SIDE CHAIN REMARK 500 10 DG A 7 0.06 SIDE CHAIN REMARK 500 10 DT A 8 0.09 SIDE CHAIN REMARK 500 10 DT A 10 0.08 SIDE CHAIN REMARK 500 10 DA B 19 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KH5 RELATED DB: PDB REMARK 900 RELATED ID: 16225 RELATED DB: BMRB DBREF 2KH6 A 1 12 PDB 2KH6 2KH6 1 12 DBREF 2KH6 B 13 24 PDB 2KH6 2KH6 13 24 SEQRES 1 A 12 DG DT DG DC DG CTG DG DT DT DT DG DT SEQRES 1 B 12 DA DC DA DA DA DC DA DC DG DC DA DC MODRES 2KH6 CTG A 6 DT HET CTG A 6 36 HETNAM CTG (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'- HETNAM 2 CTG MONOPHOSPHATE FORMUL 1 CTG C10 H17 N2 O10 P LINK O3' DG A 5 P CTG A 6 1555 1555 1.62 LINK O3' CTG A 6 P DG A 7 1555 1555 1.63 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 135 160 CONECT 160 135 161 162 163 CONECT 161 160 CONECT 162 160 CONECT 163 160 164 CONECT 164 163 165 192 193 CONECT 165 164 166 180 191 CONECT 166 165 167 CONECT 167 166 168 179 187 CONECT 168 167 169 171 CONECT 169 168 170 176 194 CONECT 170 169 195 CONECT 171 168 172 173 CONECT 172 171 CONECT 173 171 174 186 CONECT 174 173 175 176 CONECT 175 174 CONECT 176 169 174 177 178 CONECT 177 176 182 183 184 CONECT 178 176 185 CONECT 179 167 180 188 189 CONECT 180 165 179 181 190 CONECT 181 180 196 CONECT 182 177 CONECT 183 177 CONECT 184 177 CONECT 185 178 CONECT 186 173 CONECT 187 167 CONECT 188 179 CONECT 189 179 CONECT 190 180 CONECT 191 165 CONECT 192 164 CONECT 193 164 CONECT 194 169 CONECT 195 170 CONECT 196 181 MASTER 231 0 1 0 0 0 0 6 488 2 38 2 END